rs565781501
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 8P and 9B. PVS1BP6BS1BS2
The NM_001040436.3(YARS2):c.1275-2_1275-1insA variant causes a splice acceptor change. The variant allele was found at a frequency of 0.000602 in 1,613,674 control chromosomes in the GnomAD database, including 6 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0033 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00033 ( 2 hom. )
Consequence
YARS2
NM_001040436.3 splice_acceptor
NM_001040436.3 splice_acceptor
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.11
Genes affected
YARS2 (HGNC:24249): (tyrosyl-tRNA synthetase 2) This gene encodes a mitochondrial protein that catalyzes the attachment of tyrosine to tRNA(Tyr). Mutations in this gene are associated with myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2). [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PVS1
?
Splicing variant, LoF is a know mechanism of disease,
BP6
?
Variant 12-32747364-C-CT is Benign according to our data. Variant chr12-32747364-C-CT is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 215425.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=1}.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00325 (495/152286) while in subpopulation AFR AF= 0.0111 (461/41558). AF 95% confidence interval is 0.0103. There are 4 homozygotes in gnomad4. There are 234 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YARS2 | NM_001040436.3 | c.1275-2_1275-1insA | splice_acceptor_variant | ENST00000324868.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YARS2 | ENST00000324868.13 | c.1275-2_1275-1insA | splice_acceptor_variant | 1 | NM_001040436.3 | P1 | |||
YARS2 | ENST00000548490.1 | c.*286-2_*286-1insA | splice_acceptor_variant, NMD_transcript_variant | 5 | |||||
YARS2 | ENST00000551673.5 | n.172-2_172-1insA | splice_acceptor_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00327 AC: 497AN: 152168Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.000942 AC: 235AN: 249590Hom.: 1 AF XY: 0.000725 AC XY: 98AN XY: 135126
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GnomAD4 exome AF: 0.000326 AC: 477AN: 1461388Hom.: 2 Cov.: 31 AF XY: 0.000309 AC XY: 225AN XY: 727014
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GnomAD4 genome ? AF: 0.00325 AC: 495AN: 152286Hom.: 4 Cov.: 32 AF XY: 0.00314 AC XY: 234AN XY: 74466
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 07, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 11, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at